[Jmol-users] Jmol 13.0.18/13.1.18 released

[Robert H. <ha...@st...>]

I have released 13.0.18 and 13.1.18 (yes, I know I skipped 17....)

___version=13.0.18

bug fix: "ligand" should include all _g=0 (nonPDB atoms)
bug fix: POLYHEDRA with faceCenterOffset not saved in state properly; EDGES
option nonfunctional
bug fix: COMPARE could rotate to less-good fit with SMARTS search
bug fix: draw ARROW ATOM/BOND broken
bug fix: draw ARROW with offset disallows set picking draw adjustments
bug fix: concurrrent loading of two cif files by two different applets
fails
bug fix: draw LINEDATA not operative (undocumented, for state; from draw
xxx INTERSECT yyy)
bug fix: jvxl reader ignores jvxlVertexColorData
bug fix: ellipsoid rendering problems

___JmolVersion="13.1.18"

new feature: CASTEP reader filter option q=all
new feature: set picking DRAGLIGAND
  -- won't move the protein
new feature: CIF reader upgrade to allow multicharacter chain specs.
  -- See 1bgl_1bgm.cif
  -- automatically switches to chainCaseSensitive if multi-character
     or lower-case chains are read in a CIF file.
  -- note that in certain cases quotation marks will be needed:
        select chain=0123     NOT OK
        select :0123          NOT OK
        select chain="0123"   OK
        select :"0123"        OK
        select :"A*" or :"A'" or :'A"' or :"A\""
new feature: {atomset1}.distance.min({atomset2})
  -- returns an array
  -- minimum distance of each atom in atomset1 to any atom in atomset2
new feature: {atomset1}.distance.max({atomset2})
  -- returns an array
  -- maximum distance of each atom in atomset1 to any atom in atomset2
new feature: compare({atomset1} {atomset2} "ccCCN" "bonds")
new feature: {1.1}.find("ccCCN", "BONDS")
new feature: set translucent
 -- default TRUE : translucent objects are fully translucent
 -- FALSE: translucent objects are opaque to other translucent objects

bug fix: CrystalReader broken by recent change to simpleReplace()
bug fix: PyMOL movie start frame
bug fix: PyMOL putty broken
bug fix: pdbAddHydrogens may miss O3' or O5' H atoms at end of DNA strands
bug fix: pdbAddHydrogens may miss H in first group of a chain
bug fix: set defaultDrawArrowScale broken
bug fix: "ligand" should include all _g=0 (nonPDB atoms)
bug fix: applet getpropertyAsArray("bondInfo") fails
bug fix: JSmol script/scriptWait nuance with moveto.
  -- when using scriptWait with HTML5, there can be no threading
bug fix: invertSelected on trajectory causes nullPointerException
bug fix: POLYHEDRA with faceCenterOffset not saved in state properly; EDGES
option nonfunctional
bug fix: JavaScript not returning arrays properly from
Jmol.getPropertyXXXX()
  -- very important to have {} after j2sNative directive!
bug fix: COMPARE could rotate to less-good fit with SMARTS search
bug fix: draw ARROW ATOM/BOND broken
bug fix: animation MORPH broken for non-PyMOL files
 -- load trajectory ({0 6}) 1cdr.pdb
 -- animation MORPH 10
 -- animation ON
 -- load trajectory "test1.pdb" "test2.pdb"
 -- animation MORPH 30
 -- animation ON
bug fix: draw ARROW ATOM/BOND broken
bug fix: draw ARROW with offset disallows set picking draw adjustments
bug fix: concurrent loading of two cif files by two different applets fails
bug fix: draw LINEDATA not operative (undocumented, for state; from draw
xxx INTERSECT yyy)
  -- needs revision to create DATA option; can be huge and very long to
process state file
bug fix: load :2-butanone fails
bug fix: PyMOL volume map data saved from PyMOL 1.6 has slightly different
data structure
bug fix: jvxl reader ignores jvxlVertexColorData
bug fix: ellipsoid rendering problems

code: MagRes/CASTEP reader upgrades
code: color/translucent/opaque clean up in ScriptEvaluator



-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900